Ab initio molecular orbital and hybrid density functional theory calculations have been performed to study the adsorption, isomerization, and decomposition of HCN on Si(100)-2×1 using the Si9H12 cluster model of the surface. The results of our calculations indicate that the HCN can adsorb molecularly without a barrier onto the surface with both end-on (LM1) and side-on (LM2) positions. LM1 can isomerize to LM2 with a small barrier of 8 kcal/mol. The isomerization of LM2 by H-migration from C to the N atom, requires 76 kcal/mol activation energy (c.f. 47.5 kcal/mol in the gas phase) because of surface stabilization. Both HCN(a) and HNC(a) end-on adsorbates were found to dissociate readily, as concluded in our earlier experiment, to produce H and CN adspecies. The computed vibrational frequencies of HCN, CN, and also HCNH adspecies agree reasonably well with those observed experimentally. HCNH was found to be stable, with either the C or the N attaching to the surface.